In acid-base catalysis, the chemical reaction is accelerated by the addition of an acid or a base, and the acid or base itself is not consumed in the reaction. Proton transfer is the commonest reaction that enzymes perform. Proton donors and acceptors, i.e. acids and base may donate and accept protons in order to stabilize developing charges in the transition state. This typically has the effect of activating nucleophile and electrophile groups, or stabilizing leaving groups. Many acid-base catalysis reactions involve histidine because it has a pKa close to 7, allowing it to act as both an acid and a base.
Characteristics of Acid-base Catalysis
The great majority of enzyme reactions–the chemical reactions on which life depends–take place in water, under “physiological” conditions, near pH 7. Yet this is where chemical reactions are normally at their slowest. Reactive compounds are readily hydrolyzed by adding strong acid or base in vitro. But this is not a practical proposition for an enzyme: proteins are denatured in the presence of strong acid or base. Nevertheless, the way we think about catalysis by enzymes is based on our understanding of acid–base catalysis in vitro.
The acid-base catalysis is illustrated by the pH–rate profiles shown in Figure 1: the three plots are representative of the behavior of most types of substrate undergoing most sorts of reaction in water. The lower curve (I) represents the reaction in vitro of a typical, unreactive compound: it shows only acid- and base-catalyzed reactions, and reaction is very slow at the minimum, near pH 7. For the most reactive compounds, an additional feature (curve II) is a pH-independent region, where the uncatalyzed reaction with water becomes faster than the acid- and base-catalyzed reactions near neutrality. Finally, curve III is the pH–rate profile for a typical enzyme-catalyzed reaction: it is much faster than the others (signified by the break in the ordinate), and it is also qualitatively quite different, since now the rate reaches a maximum near pH 7. Enzymes are ‘designed’ to operate near pH 7, and typically show pH optima in this region, with rates falling off at higher and lower pH values.
Figure 1. Specific acid–base catalysis and enzyme catalysis compared. (Kirby A J. 2001)
The acid- and base-catalyzed reactions at high and low pH are not directly relevant to catalysis by enzymes. They typically involve activation of the substrate by the addition or removal of a proton in a rapid pre-equilibrium, followed by the rate-determining reaction of the conjugate acid or base.
Mechanism of Acid-base Catalysis
If the substrate is reactive (electrophilic) enough, activation by protonation is not necessary and the attack of water on the neutral molecule is rate determining near pH 7 (curve II of Figure 1). Formally this generates both a positive and a negative charge, and as the reaction proceeds both will be “delocalized” into the surrounding solvent via the network of hydrogen bonds. The nucleophile in a hydrolysis reaction is of course a water molecule. As the new C–O bond forms, positive charge develops on the nucleophilic oxygen, and the attached OH protons become more and more acidic, until they can be transferred to solvating water, acting formally as a general base (gb). The negative charge developing on the carbonyl oxygen may similarly be transferred via a hydrogen bond to another water molecule, acting this time as a general acid (ga). This mechanism is always available, though it does not always lead to reaction at an observable rate.
The direct reaction does have the entropic advantage of not involving a third molecule, and a carboxylate anion can–given the right conditions–displace better leaving groups than ethoxide. As long as the intermediate is more reactive than the starting material the result is catalysis of hydrolysis. This mechanism competes equally with general base catalysis for esters with a leaving group of pKa of ~7, and becomes dominant for derivatives with better leaving groups.
If the leaving group is poor it can be made viable by protonation: complete protonation to form the conjugate acid if the group is sufficiently basic, but involving partial proton transfer in the case of a weakly basic group like OR or OH. This mechanism is involved, though not easily observed, in the breakdown of the tetrahedral addition intermediates involved in the acyl transfer reactions of esters and amides.
Brønsted Acid and Base Groups in Enzymes
The “catalytic machinery” of an enzyme consists of a small number of functional groups brought together in a well-defined three-dimensional arrangement by the tertiary structure of the protein to form the active site. The functional groups concerned are a subset of those available on the side-chains of the naturally occurring amino acids. Under physiological conditions near pH 7, only weak acids and bases, with pKa within a unit or two of 7, can exist to a significant extent in the acidic or basic form. Thus the strongest acids available on amino acid side chains are the two carboxylic acids; but these will be present at pH 7 almost exclusively as the aspartate and glutamate anions–unless their pKas are perturbed by their local environment. Similarly, the strongest bases are likely to be protonated unless similarly perturbed. Although such perturbations are not uncommon, the imidazole group of histidine, because it has a pKa near 7, is at once the strongest acid and the strongest base normally available to enzymes under physiological conditions near pH 7.
A functional group involved in catalysis of a particular step of a particular reaction plays a very specific role, and so can be expected to be active in one particular ionic form: thus reactivity will depend on pH. When two (or more) such groups are involved it is common for one to be active as a general acid, in the protonated form, and the other as a general base or nucleophile, and thus in its basic form. The pH–rate dependence of the catalyzed reaction then reflects the fraction of the system with both groups in the active ionic form. At sufficiently high and low pH, a single species is present, as the free base or fully protonated form. But the fraction of the intermediate zwitterionic form increases to a maximum at a pH halfway between the two pKas. If this is the reactive form, the pH–rate profile will also show a maximum at this pH. This is the simplest explanation for a pH optimum for an enzyme-catalyzed reaction.
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